Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

VQSR on dog: error in GATK WDL pipeline


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    Laura Gauthier

    We talked about this offline, but I think it's worth documenting here for posterity (especially since the old forum with the hit you found is disappearing.) Our joint calling pipeline only runs in the cloud these days.  You'll note that the tool invoked in the GatherVcfs task is GatherVcfsCloud.  The docs claim that this tool should work locally, but the fact that the paths in the error aren't right and the fact that the NoSuchFileException is coming from the NIO library, which we use to stream data out of cloud buckets, leads me to believe something is wonky with the way it's trying to read off of your slurm setup. We don't seem to have a GatherVcfs classic anymore, but you could try removing the block in the task that has "localization_optional: true".  That will force Cromwell to copy your files to the VM (which it might not be doing now) and then hopefully from there the rest will just work.  If editing the WDL doesn't seem like it's easy peasy, you can try to confirm my hypothesis by checking the cromwell task log to see if it did actually localize your files and if it did, make sure the paths look right.  (In the cloud this is a *.log file that has things in in like "Pulling docker image" and "Running docker", but I'm not sure if you have one running locally.)

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